Estrogen receptor alpha (ERalpha) is a major regulator of metabolic processes in obesity. In this study we aimed to define the relevance of adipose tissue ERalpha during high-fat diet (HFD)-induced obesity using female aP2-Cre(-/+)/ERalpha(fl/fl) mice (atERalphaKO). HFD did not affect body weight or glucose metabolism in atERalphaKO- compared to control mice. Surprisingly, HFD feeding markedly increased mortality in atERalphaKO mice associated with a destructive bacterial infection of the uterus driven by commensal microbes, an alteration likely explaining the absence of a metabolic phenotype in HFD-fed atERalphaKO mice. In order to identify a mechanism of the exaggerated uterine infection in HFD-fed atERalphaKO mice, a marked reduction of uterine M2-macrophages was detected, a cell type relevant for anti-microbial defence. In parallel, atERalphaKO mice exhibited elevated circulating estradiol (E2) acting on E2-responsive tissue/cells such as macrophages. Accompanying cell culture experiments showed that despite E2 co-administration stearic acid (C18:0), a fatty acid elevated in plasma from HFD-fed atERalphaKO mice, blocks M2-polarization, a process known to be enhanced by E2. In this study we demonstrate an unexpected phenotype in HFD-fed atERalphaKO involving severe uterine bacterial infections likely resulting from a previously unknown negative interference between dietary FAs and ERalpha-signaling during anti-microbial defence.